[FieldTrip] Results from source analysis with different fieldtrip versions differ!?

[Schoffelen, J.M. (Jan Mathijs)]

Hi Alexandra,

Hmmm, that’s not good. We have recently tried to clean up the codebase that is doing various inverse calculations, which was indeed around the time at which you identified a change in figure quality. I don’t think this has to do with the leadfield computation.

Just as a first step, could you check whether the ‘freq’ structures are the same in the different FieldTrip versions? Just to be sure that indeed the cause of this lies in ft_sourceanalysis or ft_inverse_dics.

Best wishes,
Jan-Mathijs



> On 4 Nov 2020, at 13:38, Alexandra Steina <Alexandra.Steina at uni-duesseldorf.de> wrote:
> 
> Hello everyone,
> 
> I used the following pipeline to perform a source analysis on MEG-LFP data. I noticed different results when using different Fieldtrip Versions for the exact same data and analysis pipeline.
> I read that there was a bug in the 'ft_prepare_leadfield' function in the release of June and it says that the bug was fixed, but I got some weird results when doing dics source reconstruction on the MEG data with the Fieldtrip releases from August on (I also just tried the release from yesterday). I attached some sourceplots (all from the exact same data) that are all done with a different Fieldtrip Version.
> Does anyone know if there is still a bug in the newest fieldtrip releases or why these differences occur?
> 
>    mri  = ft_read_mri(mri_path);
>    mri.anatomy=double(mri.anatomy);
>    fidu = importdata([fidu_path,'fiducial.txt']);
>    cfg=[];
>    cfg.coordsys='neuromag';
>    cfg.method = 'fiducial';
>    cfg.fiducial.nas    = fidu.data(2,:);
>    cfg.fiducial.lpa    = fidu.data(3,:);
>    cfg.fiducial.rpa    = fidu.data(1,:);
>    real_mri=ft_volumerealign(cfg,mri);
> 
>    cfg                = [];
>    cfg.keepintermediate = 'no';
>    cfg.write          = 'no';
>    cfg.name          = [folder_intermediate,'spmtmp'];
>    segmentedmri   = ft_volumesegment(cfg, real_mri);
> 
>    cfg                = [];
>    cfg.method = 'singleshell';
>    hdm                = ft_prepare_headmodel(cfg,segmentedmri);
>    hdm = ft_convert_units(hdm,'cm');
> 
>    template = load(fullfile('fieldtrip/template/sourcemodel/standard_sourcemodel3d10mm'));
> 
>    cfg                = [];
>    cfg.grid.warpmni   = 'yes';
>    cfg.grid.template  = template.sourcemodel;  % template_grid
>    cfg.grid.nonlinear = 'yes';
>    cfg.mri            = real_mri;
>    cfg.grid.unit      ='cm';
>    grid               = ft_prepare_sourcemodel(cfg);
> 
>    cfg = [];
>    cfg.dataset = dataset;
>    cfg.dftfilter = 'yes';
>    cfg.trl = trl;
>    cfg.channel = ['MEG***2','MEG***3',Info_et.(subj).(cond).(file).bad_meg];
>    meg = ft_preprocessing(cfg);
> 
> 
>    cfg = [];
>    cfg.dataset = dataset;
>    cfg.dftfilter = 'yes';
>    cfg.trl = trl;
>    cfg.channel = Info_et.(subj).(cond).(file).old_lfp_labels;
>    cfg.montage = Info_et.(subj).(cond).(file).montage;
>    lfp = ft_preprocessing(cfg);
> 
>   data = ft_appenddata([],meg,lfp);
> 
>    cfg = [];
>    cfg.length = 1;
>    cfg.overlap = 0.5;
>    data_seg = ft_redefinetrial(cfg,data);
> 
> 
>    centerfreq = 12;
>    chan = ‘LFP-right-1-2A’;
>    bandwidth = 2;
> 
>    cfg = [];
>    cfg.method = 'mtmfft';
>    cfg.output = 'powandcsd';
>    cfg.foi = centerfreq;
>    cfg.tapsmofrq = bandwidth;
>    cfg.keeptrials = 'yes';
>    freq = ft_freqanalysis(cfg,data_seg);
> 
>    cfg=[];
>    cfg.method='dics';
>    cfg.dics.lambda='5%';
>    cfg.headmodel=hdm;
>    cfg.sourcemodel=grid;
>    cfg.frequency = centerfreq;
>    cfg.reducerank=2;
>    cfg.refchan = chan;
>    source=ft_sourceanalysis(cfg,freq);
>    source.pos = template.sourcemodel.pos;
>    source.dim = template.sourcemodel.dim;
> 
>    [maxval, maxcohindx] = max(source.avg.coh);
>    max_pos = source.pos(maxcohindx, :);
> 
>     cfg = [];
>     cfg.parameter = 'coh';
>     cfg.interpmethod        = 'nearest';
>     it = ft_sourceinterpolate(cfg,source,p); % p
> 
>     cfg =  [];
>     cfg.method = ‘ortho’;
>     cfg.funparameter = 'coh';
>     cfg.maskparameter = 'coh';
>     ft_sourceplot(cfg,it);
> 
> Thanks and greetings,
> Alexandra Steina<ft_2019.png><ft_april2020.png><ft_june2020.png><ft_november2020.png><ft_october2020.png>_______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202